Author: clopes
Date: 2012-04-13 11:41:04 -0700 (Fri, 13 Apr 2012)
New Revision: 28824
Modified:
core3/api/trunk/presentation-api/src/main/java/org/cytoscape/view/presentation/property/BasicVisualLexicon.java
core3/impl/trunk/editor-impl/pom.xml
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNestedNetworkTask.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNestedNetworkTaskFactory.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DeleteNestedNetworkTask.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DeleteNestedNetworkTaskFactory.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeAttribute.java
Log:
Changes the default value of NODE_NESTED_NETWORK_IMAGE_VISIBLE to true.
Add/DeleteNestedNetworkTasks are now disabled if the target node is a
group-node.
Modified:
core3/api/trunk/presentation-api/src/main/java/org/cytoscape/view/presentation/property/BasicVisualLexicon.java
===================================================================
---
core3/api/trunk/presentation-api/src/main/java/org/cytoscape/view/presentation/property/BasicVisualLexicon.java
2012-04-13 17:04:36 UTC (rev 28823)
+++
core3/api/trunk/presentation-api/src/main/java/org/cytoscape/view/presentation/property/BasicVisualLexicon.java
2012-04-13 18:41:04 UTC (rev 28824)
@@ -109,7 +109,7 @@
public static final VisualProperty<Boolean> NODE_SELECTED = new
BooleanVisualProperty(false, "NODE_SELECTED",
"Node Selected", true, CyNode.class);
- public static final VisualProperty<Boolean>
NODE_NESTED_NETWORK_IMAGE_VISIBLE = new BooleanVisualProperty(false,
+ public static final VisualProperty<Boolean>
NODE_NESTED_NETWORK_IMAGE_VISIBLE = new BooleanVisualProperty(true,
"NODE_NESTED_NETWORK_IMAGE_VISIBLE", "Nested Network
Image Visible", CyNode.class);
// ///// Edge VP ///////
Modified: core3/impl/trunk/editor-impl/pom.xml
===================================================================
--- core3/impl/trunk/editor-impl/pom.xml 2012-04-13 17:04:36 UTC (rev
28823)
+++ core3/impl/trunk/editor-impl/pom.xml 2012-04-13 18:41:04 UTC (rev
28824)
@@ -97,7 +97,7 @@
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
- <artifactId>vizmap-gui-api</artifactId>
+ <artifactId>group-api</artifactId>
</dependency>
<dependency>
<groupId>junit</groupId>
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNestedNetworkTask.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNestedNetworkTask.java
2012-04-13 17:04:36 UTC (rev 28823)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNestedNetworkTask.java
2012-04-13 18:41:04 UTC (rev 28824)
@@ -2,15 +2,17 @@
import java.util.ArrayList;
+import java.util.List;
+import org.cytoscape.group.CyGroupManager;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.task.AbstractNodeViewTask;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.BasicVisualLexicon;
-import org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.ProvidesTitle;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
@@ -21,7 +23,7 @@
public class AddNestedNetworkTask extends AbstractNodeViewTask {
- private final SelectedVisualStyleManager svsmMgr;
+ private final VisualMappingManager vmMgr;
private static final Logger logger =
LoggerFactory.getLogger(AddNestedNetworkTask.class);
@@ -36,24 +38,26 @@
public AddNestedNetworkTask(final View<CyNode> nv,
final
CyNetworkView view,
final
CyNetworkManager mgr,
- final
SelectedVisualStyleManager svsmMgr) {
+ final
VisualMappingManager vmMgr,
+ final
CyGroupManager grMgr) {
super(nv,view);
- this.svsmMgr = svsmMgr;
+ this.vmMgr = vmMgr;
- nestedNetwork = new ListSingleSelection<CyNetwork>(new
ArrayList<CyNetwork>(mgr.getNetworkSet()));
+ final List<CyNetwork> networks = new
ArrayList<CyNetwork>(mgr.getNetworkSet());
+ nestedNetwork = new ListSingleSelection<CyNetwork>(networks);
final CyNetwork netPointer =
nodeView.getModel().getNetworkPointer();
- if (netPointer != null)
+ if (netPointer != null && networks.contains(netPointer))
nestedNetwork.setSelectedValue(netPointer);
}
@Override
public void run(TaskMonitor tm) throws Exception {
- final CyNode n = nodeView.getModel();
- n.setNetworkPointer(nestedNetwork.getSelectedValue());
+ final CyNode node = nodeView.getModel();
+ node.setNetworkPointer(nestedNetwork.getSelectedValue());
-
nodeView.setLockedValue(BasicVisualLexicon.NODE_NESTED_NETWORK_IMAGE_VISIBLE,
Boolean.TRUE);
- svsmMgr.getCurrentVisualStyle().apply(netView);
+ final VisualStyle style = vmMgr.getVisualStyle(netView);
+ style.apply(netView);
netView.updateView();
}
}
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNestedNetworkTaskFactory.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNestedNetworkTaskFactory.java
2012-04-13 17:04:36 UTC (rev 28823)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/AddNestedNetworkTaskFactory.java
2012-04-13 18:41:04 UTC (rev 28824)
@@ -1,26 +1,31 @@
package org.cytoscape.editor.internal;
+import org.cytoscape.group.CyGroupManager;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.task.AbstractNodeViewTaskFactory;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.TaskIterator;
public class AddNestedNetworkTaskFactory extends AbstractNodeViewTaskFactory {
final CyNetworkManager netMgr;
- final SelectedVisualStyleManager svsmMgr;
+ final VisualMappingManager vmMgr;
+ final CyGroupManager grMgr;
- public AddNestedNetworkTaskFactory(final CyNetworkManager netMgr, final
SelectedVisualStyleManager svsmMgr) {
+ public AddNestedNetworkTaskFactory(final CyNetworkManager netMgr,
+
final VisualMappingManager vmMgr,
+
final CyGroupManager grMgr) {
this.netMgr = netMgr;
- this.svsmMgr = svsmMgr;
+ this.vmMgr = vmMgr;
+ this.grMgr = grMgr;
}
@Override
public TaskIterator createTaskIterator(View<CyNode> nodeView,
CyNetworkView networkView) {
- return new TaskIterator(new AddNestedNetworkTask(nodeView,
networkView, netMgr, svsmMgr));
+ return new TaskIterator(new AddNestedNetworkTask(nodeView,
networkView, netMgr, vmMgr, grMgr));
}
@Override
@@ -32,8 +37,9 @@
// Nodes with unregistered network pointers should be ignored
because they are probably being used as something
// else other than regular nested networks (e.g. groups).
final CyNode node = nodeView.getModel();
+ final CyNetwork net = networkView.getModel();
final CyNetwork netPointer = node.getNetworkPointer();
- return netPointer == null ||
netMgr.networkExists(netPointer.getSUID());
+ return ( netPointer == null ) || (
netMgr.networkExists(netPointer.getSUID()) && !grMgr.isGroup(node, net) );
}
}
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java
2012-04-13 17:04:36 UTC (rev 28823)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CyActivator.java
2012-04-13 18:41:04 UTC (rev 28824)
@@ -5,13 +5,13 @@
import java.util.Properties;
import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.group.CyGroupManager;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.service.util.AbstractCyActivator;
import org.cytoscape.task.NetworkViewLocationTaskFactory;
import org.cytoscape.task.NetworkViewTaskFactory;
import org.cytoscape.task.NodeViewTaskFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
-import org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager;
import org.osgi.framework.BundleContext;
@@ -24,13 +24,13 @@
public void start(BundleContext bc) {
CyNetworkManager cyNetworkManagerServiceRef =
getService(bc,CyNetworkManager.class);
CyEventHelper cyEventHelperServiceRef =
getService(bc,CyEventHelper.class);
- VisualMappingManager vmm =
getService(bc,VisualMappingManager.class);
- SelectedVisualStyleManager selectedVisualStyleManagerServiceRef
= getService(bc,SelectedVisualStyleManager.class);
+ VisualMappingManager visualMappingManagerServiceRef =
getService(bc,VisualMappingManager.class);
+ CyGroupManager cyGroupManagerServiceRef =
getService(bc,CyGroupManager.class);
SIFInterpreterTaskFactory sifInterpreterTaskFactory = new
SIFInterpreterTaskFactory();
- NetworkViewLocationTaskFactory networkViewLocationTaskFactory =
new AddNodeTaskFactory(cyEventHelperServiceRef, vmm);
- NodeViewTaskFactory addNestedNetworkTaskFactory = new
AddNestedNetworkTaskFactory(cyNetworkManagerServiceRef,
selectedVisualStyleManagerServiceRef);
- NodeViewTaskFactory deleteNestedNetworkTaskFactory = new
DeleteNestedNetworkTaskFactory(cyNetworkManagerServiceRef,
selectedVisualStyleManagerServiceRef);
+ NetworkViewLocationTaskFactory networkViewLocationTaskFactory =
new AddNodeTaskFactory(cyEventHelperServiceRef, visualMappingManagerServiceRef);
+ NodeViewTaskFactory addNestedNetworkTaskFactory = new
AddNestedNetworkTaskFactory(cyNetworkManagerServiceRef,
visualMappingManagerServiceRef, cyGroupManagerServiceRef);
+ NodeViewTaskFactory deleteNestedNetworkTaskFactory = new
DeleteNestedNetworkTaskFactory(cyNetworkManagerServiceRef,
visualMappingManagerServiceRef, cyGroupManagerServiceRef);
Properties sifInterpreterTaskFactoryProps = new Properties();
sifInterpreterTaskFactoryProps.setProperty("enableFor",
"networkAndView");
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DeleteNestedNetworkTask.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DeleteNestedNetworkTask.java
2012-04-13 17:04:36 UTC (rev 28823)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DeleteNestedNetworkTask.java
2012-04-13 18:41:04 UTC (rev 28824)
@@ -6,8 +6,8 @@
import org.cytoscape.task.AbstractNodeViewTask;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.BasicVisualLexicon;
-import org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -15,16 +15,16 @@
public class DeleteNestedNetworkTask extends AbstractNodeViewTask {
- private final SelectedVisualStyleManager svsmMgr;
+ private final VisualMappingManager vmMgr;
private static final Logger logger =
LoggerFactory.getLogger(DeleteNestedNetworkTask.class);
public DeleteNestedNetworkTask(final View<CyNode> nv,
final
CyNetworkView view,
final
CyNetworkManager mgr,
- final
SelectedVisualStyleManager svsmMgr) {
+ final
VisualMappingManager vmMgr) {
super(nv,view);
- this.svsmMgr = svsmMgr;
+ this.vmMgr = vmMgr;
}
@Override
@@ -32,8 +32,8 @@
final CyNode n = nodeView.getModel();
n.setNetworkPointer(null);
-
nodeView.clearValueLock(BasicVisualLexicon.NODE_NESTED_NETWORK_IMAGE_VISIBLE);
- svsmMgr.getCurrentVisualStyle().apply(netView);
+ final VisualStyle style = vmMgr.getVisualStyle(netView);
+ style.apply(netView);
netView.updateView();
}
}
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DeleteNestedNetworkTaskFactory.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DeleteNestedNetworkTaskFactory.java
2012-04-13 17:04:36 UTC (rev 28823)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/DeleteNestedNetworkTaskFactory.java
2012-04-13 18:41:04 UTC (rev 28824)
@@ -1,26 +1,31 @@
package org.cytoscape.editor.internal;
+import org.cytoscape.group.CyGroupManager;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.task.AbstractNodeViewTaskFactory;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager;
+import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.TaskIterator;
public class DeleteNestedNetworkTaskFactory extends
AbstractNodeViewTaskFactory {
final CyNetworkManager netMgr;
- final SelectedVisualStyleManager svsmMgr;
+ final VisualMappingManager vmMgr;
+ final CyGroupManager grMgr;
- public DeleteNestedNetworkTaskFactory(final CyNetworkManager netMgr,
final SelectedVisualStyleManager svsmMgr) {
+ public DeleteNestedNetworkTaskFactory(final CyNetworkManager netMgr,
+
final VisualMappingManager vmMgr,
+
final CyGroupManager grMgr) {
this.netMgr = netMgr;
- this.svsmMgr = svsmMgr;
+ this.vmMgr = vmMgr;
+ this.grMgr = grMgr;
}
@Override
public TaskIterator createTaskIterator(View<CyNode> nodeView,
CyNetworkView networkView) {
- return new TaskIterator(new DeleteNestedNetworkTask(nodeView,
networkView, netMgr, svsmMgr));
+ return new TaskIterator(new DeleteNestedNetworkTask(nodeView,
networkView, netMgr, vmMgr));
}
@Override
@@ -32,8 +37,9 @@
// Nodes with unregistered network pointers should be ignored
because they are probably being used as something
// else other than regular nested networks (e.g. groups).
final CyNode node = nodeView.getModel();
- final CyNetwork netPointer = node.getNetworkPointer();
+ final CyNetwork np = node.getNetworkPointer();
+ final CyNetwork network = networkView.getModel();
- return netPointer != null &&
netMgr.networkExists(netPointer.getSUID());
+ return np != null && netMgr.networkExists(np.getSUID()) &&
!grMgr.isGroup(node, network);
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeAttribute.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeAttribute.java
2012-04-13 17:04:36 UTC (rev 28823)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleNodeAttribute.java
2012-04-13 18:41:04 UTC (rev 28824)
@@ -29,7 +29,6 @@
import org.cytoscape.io.internal.read.xgmml.ParseState;
import org.cytoscape.model.CyNode;
-import org.cytoscape.view.presentation.property.BasicVisualLexicon;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
@@ -63,9 +62,6 @@
final String netId =
atts.getValue("value");
final CyNode node =
manager.getCurrentNode();
manager.getCache().addNetworkPointer(node, netId);
- // Also add this visual property, so
the network pointer is displayed as a regular nested network.
- manager.addGraphicsAttribute(node,
-
BasicVisualLexicon.NODE_NESTED_NETWORK_IMAGE_VISIBLE.getIdString(), "true");
}
}
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